Very little chemical information is known about substances being abused in South-Africa. This can be attributed to the fact that possession of drugs constitutes a criminal offence. Not much research is done, and with the exception of self-reported, rehabilitation institution data, from the South African Community Epidemiology Network on Drug Use (SACENDU) and the South African Police drug related arrest data, no other data on drugs and drug use, is publically available. Drugs are being manufactured from legal and illegal chemicals in clandestine laboratories, not complying with any health, safety or quality standards causing a serious health risk in communities. The strategy for the fight against drug abuse in South Africa, the National Drug Master Plan 2013-2017 (NDMP), is compiled by the Central Drug Authority (CDA). Without proper research, data to base decisions and strategies on and proper measuring of achievements, the implementation of the plan suffers as a consequence. The Forensic Science Laboratory (FSL) of the South African Police Service (SAPS), is responsible for the chemical testing of substances, suspected of being illegal drugs, for identification purposes. This supports the prosecuting of suspects during criminal procedures. With the active ingredient known, the use of street names e.g. Tik, Choef or Speed (all referring to methamphetamine) can be abandoned and confusion and misconceptions eliminated. This pilot study investigates the arrest data, in combination with the charge laid against the arrestee and the chemically identified active ingredient in each case. Arrest data revealed a 400% increase in drug related arrests over the last 10 years, while the NDMP requires a 10% decrease. It further highlights the fact that the measurement of success (number of arrests) in the SAPS, resulted in a focus on arresting persons in possession of drugs. The dealers and manufacturers were not adequately addressed and prevention, through chemical monitoring, suffered as a result. This study also clearly revealed that international trends are not a definite indication of the extent and type of drug abuse in South African Communities. The study further attempts to contribute, and to better describe the situation of drugs and drug abuse in communities. This in turn, will provide data to develop evidence based strategies, designed to meet the defined needs of communities, one of the aspects highlighted by the minister in the NDMP, namely an intervention based on reality and local statistics. It is therefore clear that a scientific understanding of the composition of abused substances can direct treatment, policy, prevention measures and provide intelligence to combat drug abuse and illegal drug manufacturing in South Africa.

Background: Sudden unexpected death in infancy (SUDI) is among the most frequent causes of mortality in infants less than one year of age. Respiratory infections have been identified as the most frequent cause of death in these infants. Yet, the broad range of respiratory pathogen that might be involved in SUDI is poorly studied. This study aimed to investigate the incidence of the respiratory pathogens in SUDI. Methods: A prospective study was carried out on SUDI cases admitted to Salt River Forensic Pathology Laboratory from February 2015 through May 2015. Cerebrospinal fluid, pericardial fluid and lung biopsy were collected from each study participant during post-mortem examination. Total nucleic acids were extracted on the automated QIAsymphony platform. The microbial diversity was investigated using a commercialized multiplex real-time PCR assay, the "FTD Respiratory pathogens 33" kit. This assay is able to detect 21 viruses, 11 bacteria and one fungus. In each real-time PCR run, a positive and non-template sterile water were included as controls. Results: Thirty SUDI cases (median age, 3 (interquartile range (IQR): 2 - 8 months) were included in the study. Twenty participants were males. Positive microbiological results from at least one of the three samples were obtained in 28 cases (93%). According to the type of sample, respiratory pathogens were detected in almost all the lung biopsies (93%), while it was only detected in 60% and 50% of the cerebrospinal and the pericardial fluids, respectively. The median cycle threshold value was lower in lung biopsies (30 (IQR: 28 ‒ 35)) compared to both cerebrospinal (34 (IQR: 30 ‒ 36)) and pericardial fluids (35 (IQR: 33 ‒ 35)) (p= 0.039). In lung biopsies, the most commonly detected bacteria were K. pneumoniae (47%, 14/30) and M. catarrhalis (20%, 6/30). H. influenza (7%, 2/30) and M. pneumoniae (7%, 2/30) were the bacteria often detected in pericardial fluid and cerebrospinal fluid, respectively. Human Metapneumovirus was the most frequently virus detected in all three sample types assessed, accounting for 33% (10/30) in cerebrospinal fluid, 37% (11 /30) in pericardial fluid and 57% (17/30) in lung biopsy samples, respectively. A single type of pathogen was detected n seven of the 28 positive cases. Conclusion: This study highlights the potential implication of respiratory infection in SUDI and it reports one of the highest incidences of respiratory pathogens in SUDI cases. In addition, it is the first to report the high incidence rate of Human Metapneumovirus in SUDI cases. The findings also showed that the majority of SUDI cases are associated with synergetic interaction of multiple respiratory infections. However, data related to histopathology and bacterial culture were not available. A broad range of respiratory pathogens should be included in the routine investigation of SUDI cases with more sensitive diagnostic methods.

The burden of unresolved crime in South Africa highlights the need to improve methods of identifying perpetrators of crimes. One globally accepted method for human identification is forensic DNA profiling. Since trace evidence is often retrieved in small amounts, the optimal recovery of DNA from these samples is crucial. Methods for the recovery of touch DNA from swabs typically make use of a spin basket or filter, combined with a centrifugation step, to enhance the release of cells from the swab prior to DNA extraction. The NucleoSpin® Forensic Filter (Macherey-Nagel, Düren) is one such example, but it has not been thoroughly assessed on touch DNA samples. This study aimed to assess if the inclusion of the NucleoSpin® Forensic Filter significantly improved DNA recovery and DNA profiling success from cotton and flocked swabs used to collect touch DNA and buccal cells (control). Buccal cells and touch DNA samples were collected from 25 volunteers using each swab type (cotton and flocked) in duplicate. DNA was extracted from the samples using the NucleoSpin® DNA Forensic kit, one set with, and the other set without, NucleoSpin® Forensic Filters. DNA concentration was assessed using Qubit™ fluorometry and qPCR, and DNA profiling was done using the PowerPlex® ESX 16 system. The inclusion of the NucleoSpin® Forensic Filters significantly improved DNA concentration in buccal cells collected using flocked swabs (p = 0.035). However, no significant differences were noted for touch DNA samples, for either swab type. There was also no significant difference in DNA profiling success when NucleoSpin® Forensic Filters were used, regardless of swab and sample type. These results suggest that the NucleoSpin® Forensic Filters should not be included in the DNA extraction workflow, particularly for touch DNA samples. With only 16 % of touch DNA samples yielding full DNA profiles, there is the need to improve DNA recovery. Factors such as swab type and swab preservation buffers, should be investigated in future research.

A retrospective case review revealed an increase in sudden unexpected death (SUD) admittance at Salt River Mortuary (SRM) between 2014 and 2018, and that 40 % of SUD occurred in young individuals between the ages of 1 and 40 years old (SUDY). Despite extensive investigations, the cause of death remained undetermined in 26 % of SUDY cases. These dormant cases may benefit from retrospective post-mortem molecular autopsies for investigation into genetic causes of death. Often, formalin fixed paraffin embedded tissues (FFPETs) are the only archival sources of DNA available for retrospective analyses. This study aimed to optimise DNA recovery from FFPETs for potential use in molecular autopsies of unresolved SUDY cases. To this end, DNA was extracted from FFPET sections using the QIAamp® DNA FFPE tissue kit; the thickness and number of sections were varied. DNA was assessed using spectrophotometry, real-time PCR and digital capillary electrophoresis. Results showed that finer sectioning (1-µm thick as compared to 3-µm and 5-µm thick), improved DNA concentrations, purities and DNA fragment lengths. Increasing the number of 1-µm thick sections from 30 to 100, significantly improved DNA yield. DNA was not significantly more degraded for FFPETs stored for up to three years, which holds promise in the effectiveness of the technique for aged samples. The DNA extraction method developed in this study yielded a median of 320 ng (287 ng - 698 ng) of DNA with 55 % of DNA fragments being at least 400 bp in size. These results are especially informative for downstream molecular analyses, indicating that genotyping or sequencing assays need to be designed to target amplicons less than 400 bp in size. The degraded nature of the FFPET samples also suggests that massively parallel sequencing might be suited for downstream molecular analysis for determining cause of death in unresolved SUDY cases.

Road traffic collisions (RTCs) are a major contributor to unnatural death worldwide, but especially in low-to-middle-income countries (LMICs) where motorised transport has rapidly expanded. A literature review into RTCs and alcohol indicated that it is well recognised that alcohol intoxication is a key risk factor in RTCs and road traffic fatalities (RTFs). It also indicated that literature concerning the role of alcohol intoxication in RTFs in South Africa is limited. Hence, this study aimed to investigate alcohol in RTF victims in five of the major mortuaries (Salt River, Tygerberg, Paarl, Worcester and George) in the Western Cape Province between 1 January 2016 and 31 December 2017. Cases were extracted from the Western Cape Forensic Pathology Service (FPS) internal database, which included demographic and crash information, together with blood alcohol concentration (BAC) results. In total, 2079 cases over the two years were included in the study, with most cases admitted in the metropole of Cape Town (Salt River: n=838, Tygerberg: n=693). The proportion of unnatural deaths were greater outside the metropole (George, Worcester and Paarl) compared to the metropole (Salt River and Tygerberg) areas. The majority of fatalities were male individuals (male to female ratio of 3.52:1), with the average age of 35.2 ± 17.2 years. Most victims were pedestrians (n = 1106; 53.7%) and dark wet roads, and highways were noted as risk factors in RTFs. Blood was submitted for alcohol analysis in 1432 (68.9%) cases, and results were available for 1314 (91.8%) cases. Of the available results, 709 cases (54%) were positive for alcohol (BAC of ≥ 0.01g/100 mL). Of the positive cases, most had a BAC between 0.15 and 0.29 g/100mL and the overall average BAC was 0.20 g/100 mL. Pedestrians and drivers had the highest median BACs, and almost a third of all the positive BAC results were from pedestrian deaths. The findings of this dissertation can contribute to the growing research on alcohol and injury in South Africa, especially as it relates to RTFs. Insight into vulnerable populations within the province is highlighted, together with key risk factors associated with RTFs, as well as safety measures that may be targeted for improvement, especially with regards to driving and walking on the roads while intoxicated.

Homicide is one of the leading causes of death in South Africa. Homicides as a result of a firearm, sharp instrument or blunt object, may all potentially inflict severe cranial trauma. Often the lateral aspect of the cranium is fractured in homicidal assaults, however, the focus of head injury biomechanics has been the frontal bone. This is due to automotive-related incidents. Thus it is important for researchers to broaden their knowledge on lateral head impacts. This data could ultimately act as a tool in making cranial bone trauma analysis less subjective in nature. This minor dissertation discusses human cranial bones and explores different types of cranial fractures. It further provides an in depth discussion on the different types of experimental tests and specimens used in biomechanical testing. A current review on the literature surrounding head impacts is also provided. The research conducted for this minor dissertation uses the Cape (Chacma) Baboon as a model to attempt to simulate cranial blunt trauma observed in human bone. Fifteen Cape (Chacma) Baboon head specimens were subjected to a single temporo-parietal impact. These specimens were impacted with an aluminium striker bar that resembles the dimensions of a hammer (length: 23cm, circumference: 40cm and weight: 200g). The aim of these hammer tests were to characterise soft and hard tissue wound morphology as a result of blunt cranial impacts. Resulting data was analysed to determine if a significant correlation existed between impact velocity or energy and the extent of trauma observed. The remaining twelve Cape (Chacma) Baboon specimens were all subjected to a single impact in the temporo-parietal region. These specimens were impacted with a Hopkinson pressure bar, which is manufactured from the same material as the striker bar. The aim of the Hopkinson pressure bar tests was to attempt to determine the force of impact. The use of the Hopkinson pressure bar to determine fracture forces in baboon head specimens is novel. The fracture forces obtained in the current study compare well with literature investigating lateral impacts. Furthermore, the fracture patterns obtained in the current study realistically simulate cranial trauma seen in humans. It would therefore be beneficial to advance research using the baboon model and Hopkinson pressure bar apparatus.

The identification of bodily fluids for forensic purposes is typically classified as either presumptive or confirmatory. Presumptive tests (PT) are conducted first to screen for certain compounds which are relatively specific to particular fluids. Confirmatory tests are used to confirm the identity of a body fluid. Semen is one of the most common bodily fluids encountered in sexual assault cases and contains high concentrations of the acid phosphatase (AP) enzyme. The brentamine FB reagent reacts with the AP that is present in semen, and turns purple. If the colour change is observed within a specific time threshold, it is considered presumptively positive for semen. Cut-off time varies considerably between forensic laboratories, but in South Africa, the cut-off time is defined as 65 seconds. Additionally, semen may be considered to be from human origin if it reacts within 50 seconds. These cut off times have been arbitrarily defined, and there is little research in a local context to substantiate or inform the threshold time for the brentamine FB test for semen. Therefore this study assessed the sensitivity, specificity and kinetics of the brentamine FB test on semen from South African male volunteers (n=15), canines (n=2) and various fruit extracts and compared these results to purified human AP. Each semen sample was subjected to the PT in an indirect and direct method, and these tests were performed both on fresh and aged samples. The majority of fruit extracts yielded a distinctly different colour change compared to the purple that was produced from semen except for mushroom which also turned purple. Absorbance spectroscopy was used to determine the rate of the reaction at 525 nm. There were no significant differences between the rate of reaction for fresh and aged samples using both direct and indirect testing.

Molecular phenotyping is the use of informative genetic variation to estimate appearance. This concept can be applied in a forensic context to predict the appearance of suspects or decayed deceased individuals, which would otherwise remain unidentifiable. This concept has importance in a local context, as approximately 300 individuals remain unidentified, after conventional identification techniques, at Salt River Mortuary, every year. Ancestry Informative Markers (AIMs) are genetic variants with DNA which have been commonly associated with pigmentation phenotypes, and thus has value in predicting skin tone, hair colour and eye colour. This research study aimed to design and optimise an assay to genotype 13 AIMs associated with pigmentation, and then demonstrate the value of this assay by applying it to a case example and qualitatively predicting appearance. Primers were designed and PCR assays optimised to amplify each region, followed by Sanger sequencing on a case example. The case was that of an abandoned neonate, with unknown sex and ancestry. A comparison of the obtained genotypes to previous literature was performed to qualitatively estimate the skin tone, eye colour and hair colour of the decedent, which was not only in agreement with the forensic pathologist’s interpretation of sex and ethnicity, but provided richer detail with regards to ancestry, skin tone, eye colour and hair colour. The PCR assays were then further optimised into four multiplex assays with the intention of genotyping these AIMs by two SNaPshot® PCR assays (Applied Biosystems) in a larger control cohort to model the relationship between these AIMs and melanin index more objectively. Unfortunately, the scope of this research project did not allow for the completion of this additional aspect. Overall, these results indicate that these 13 AIMs have potential to predict pigmentation phenotypes of South African individuals. However, genotyping and modelling of the effects of these AIMs should be performed on a large cohort to further strengthen this conclusion.

Pesticide-related poisonings place a burden on the public health system in low- and middleincome countries. Notification of pesticide poisonings and deaths is a legal requirement in South Africa, however, our understanding of the prevalence and type of pesticides involved in poisoning cases remains limited. This is further complicated by the emergence of ‘street pesticides', which are unlabelled and illegally sold toxic pesticides. It is important to understand the role of these and other pesticides in local poisonings, and mortuary data provides an important resource to be able to investigate pesticide-related mortality specifically. This study aimed to build on previous research conducted at the Salt River mortuary (SRM) by expanding and updating our understanding of pesticide-related fatalities within the West Metropole of Cape Town. A retrospective, cross-sectional review of all unnatural death cases admitted to the SRM between January 2016 and December 2019 (inclusive) was conducted so as to identify pesticide-related deaths for further investigation. A total of 15 761 cases were admitted to SRM over the 4-year study period (mean: 3941 cases per annum). From this total, 92 cases (0.58%) were identified as pesticide related. Most decedents were male (59.8%), with the cohort's mean age being 26.2 years (range: 2 months to 66 years). The majority of cases were suicides (60.8%), and terbufos (an organophosphate) was detected in 50 cases (54.3%). Pesticiderelated fatalities were found to predominately occur in lower socio-economic areas. According to the data adults and adolescents are most at risk of being exposed to the harmful effects of these harmful compounds. Using a holistic approach to investigating pesticide-related fatalities could provide important clues that assist in gaining a better understanding of the factors that influence pesticide-related incidents. Combined efforts from healthcare practitioners and forensic investigators could help inform policy-makers on ways to minimise the use or distribution of pesticide compounds.

Fire-related fatalities pose many investigative challenges, in part due to their fragility. This can be managed with the creation of protocols, specific to the environment in which they are implemented. Currently, no protocol for the recovery and handling of fire-related fatalities exists in Cape Town, South Africa. Additionally, the challenges, risk factors, and resources present at forensic scenes in the area have not been documented. From April to December of 2015, fire-related death scenes were attended with Salt River Forensic Pathology Laboratory, which serves the West Metropole of Cape Town. Details of the fatal fire scenes were noted, including the challenges faced, and the settings in which the fires occurred. Emphasis was placed on methodologies used to recover, handle, and transport remains, and the availability and utilisation of resources. The affect these methodologies had on the condition of the remains between scene and autopsy was assessed. In total 32 fire-related death scenes were attended, with 48 decedents recovered. Males predominated (64.6%), and the majority were young adults (75%). Accidental deaths were most prevalent (79.2%), however a fire-related suicide and homicides highlighted the importance of thorough investigation. Informal housing constituted 68.8% of the fatal fire scenes and presented unique scene constraints, including no direct road access at 50% of these scenes. Investigative limitations included: inadequate interagency communication, resulting in a lack of collateral information available at autopsy; deficient scene and contextual documentation; non-standardised recovery methodologies; insufficient availability and utilisation of resources (including safety equipment); and no specialised personnel (e.g. forensic pathologists/ anthropologists) conducting scene recovery. The majority of cases (60.4%) were further fragmented or fractured by time of autopsy, illustrating the necessity for improvement of current methodologies and the importance of the involvement of forensic anthropologists in recovery of fragmentary remains.